Also copy [mysqld] section to [embedded]

mysql-test/include/default_mysqld.cnf:
  Use --slave-net-timeout instead of --set-variable=slave_net_timeout

mysql-test/include/default_mysqld.cnf

@@ -15,7 +15,7 @@ max_heap_table_size=        1M
 
 loose-innodb_data_file_path=      ibdata1:10M:autoextend
 
-set-variable=               slave_net_timeout=120
+slave-net-timeout=120
 
 log-bin
 

mysql-test/lib/My/ConfigFactory.pm

@@ -349,22 +349,27 @@ sub post_check_client_groups {
 
 #
 # Generate [embedded] by copying the values
-# needed from first [mysqld.<suffix>]
+# needed from the default [mysqld] section
+# and from first [mysqld.<suffix>]
 #
 sub post_check_embedded_group {
   my ($self, $config)= @_;
 
   return unless $self->{ARGS}->{embedded};
 
+  my $mysqld= $config->group('mysqld') or
+    croak "Can't run with embedded, config has no default mysqld section";
+
   my $first_mysqld= $config->first_like('mysqld.') or
     croak "Can't run with embedded, config has no mysqld";
 
   my @no_copy =
     (
      'log-error', # Embedded server writes stderr to mysqltest's log file
+     'slave-net-timeout', # Embedded server are not build with replication
     );
 
-  foreach my $option ( $first_mysqld->options() ) {
+  foreach my $option ( $mysqld->options(), $first_mysqld->options() ) {
     # Don't copy options whose name is in "no_copy" list
     next if grep ( $option->name() eq $_, @no_copy);